Phantasm Reborn
by darkmoonvampire
Summary: Physically speaking she was in perfect health, but her mind was a different matter. There's only so much a person can take before their mind snaps, their reality bent so much that it no longer stands straight. Her journey home is only just beginning. Can John succeed in making her whole again? Elizabeth x John.
1. In The Dark

Chapter 1: In the Dark

It was by pure luck that they found her.

It had started out as a standard exploration mission, scout the planet and see if there were any locals and if they wanted to trade. The easiest mission in the book, or at least that was what they were expecting. Just an ordinary day out in the Pegasus Galaxy.

Except that it turned out to be rather extraordinary and quite frankly one of the happiest days the team had experienced in a long time. For today it was the day that they wound discover a lost friend that they believed to have perished.

They were walking aimlessly around in the forest just seeing if held any minerals or produce that would help feed the populace of Atlantis, when Rodney detected strange low levelled energy readings. Naturally they ventured in the direction he pointed, with Sheppard on point and Ronan bringing up the rear while Rodney talked Teyla's ear off in the middle.

It didn't take them long to discover a cave seemingly inconspicuous in its appearance. Then Rodney said he recognized the energy signature as Asurans but still no detection of any Replicators around.

"I thought they were all blown up." Ronan remarked dryly, leaning against the right hand entrance of the cave.

"They were." Rodney replied exasperatedly and sighed heavily as he clutched his weapon tighter to his chest. He was stood next to Ronan, who was looking at him disapprovingly and flipped his gun to the kill setting.

"Let's find out for definite, shall we?" Sheppard said from the left hand side of the entrance to the cave with Teyla at his side, who remained silent but nodded that she was ready whenever they were.

Weapons at the ready they cautiously entered the cave simultaneously and manoeuvred round the dank dark corners. Slowly the cave formation changed into the familiar design and architecture of the Asuran patterns and walls. Lights flickered on at their presence and the energy levels increased slightly as the facility slowly came back to life. Their uneasiness only grew when they continued to traverse the long corridor and encountered no sign of Replicators.

It was obvious that they were heading further and further underground, which explained why they had barely detected the energy signals in the first place. They were just starting to wonder if there was actually any end to the passageway when they spotted a closed door. They approached it, wary of what could be lurking on the other side.

"I'm not detecting any Replicators. Just a single life sign, very faint and the power output seems to be localised here too." Rodney read out from his little hand held scanner.

"A life sign? Who would possibly be down here?" Teyla asked incredulously and they all frowned when they could come up with no answer.

"Whoever it is, they're about to get a surprise." Ronan stated and flipped his gun back to stun mode and waited for Sheppard's signal.

"Let's go say hello." Sheppard remarked and waved his hand over the door control and walked through to the greatest surprise of all.

The room was roughly the same size of the Gate room, but it was dimly lit and the colours were more dark blue and purple than the bright fluorescents they were used to. The room was packed with machines that appeared to be some form of data servers and dozens of thick wires ran from each one, littering the floor in a jumbled mess. They were intricately woven through each other, connecting to various other machines but some lead to the very centre of the room.

The team couldn't believe their eyes. There in the middle was a chamber that resembled the status chambers they had discovered in the city. But it was what was contained in it that had them all stopped in their tracks, all normal thought process out of the proverbial window.

She appeared to be unharmed, merely asleep and she looked exactly the same as she did the last time they saw her. She was wearing the same clothes, the dark grey/navy blue uniform that she had put of haphazardly when they went to their mission. It felt like an eternity since they had all last seen her face when it had only been just over a year.

"Elizabeth..." Sheppard's voice whispered as if he was saying a prayer. His brows furrowed and a million emotions on slaughtered his body, completely unprepared at the very sight of her.

"But-but-but- They said she was dead!" Rodney exclaimed hysterically and started frantically searching the various computers and machines, trying to verify that it was indeed their friend how to disconnect her.

"They must have lied." Teyla's voice was gentle but it sounded as though it could break at any moment, such as they joy was at finding Elizabeth.

"Unless it's not really her." Ronan suggested and lowered his gun if only by a margin. When the three of them just looked at him in disbelief he added "It wouldn't be the first we came across a copy." He shrugged hopping that it would somehow alleviate their shock at his suggestion.

"Copy or not, it's Elizabeth and we need to get her home. I'll be damned if we just leave her again." Sheppard's voice raised an octave or more, clearly showing that the decision had been made.

"Ok, so I think I can disconnect her, plus I believe I can download the data on what exactly this place is." Rodney said as his fingers started tapping away hurriedly onto the computer interface. "You might want to catch her; I don't think it's going to be gentle." He offered as he pressed the release command.

The chamber started to hiss and smoke and fumes vented out into the room as it unlocked the hatch. It didn't take long for the lights in the chamber to switch off completely and the glass frame swung to one side.

Sheppard reacted instantly, unclasping his P-90 and handing to Teyla before taking the few steps quickly to stand in front of Elizabeth and catch her in his arms as she slumped unconsciously forward. John had to go down on his knees to wrap one arms around her waist tightly, pressing her against him.

"I've got you." He spoke gently even though he knew she couldn't hear him. Using his other hand he pressed two fingers to her neck and sighed with relief when he felt a steady rhythm beat underneath. Then he placed his free hand under her knees and stood up, holding her bridal style, and making sure her head rested comfortably in his shoulder.

"We've got her." Teyla remedied as she smiled softly and handed his weapon for Ronan to dual wield along with his pistol.

"Hopefully with this, we can find out what happened to her." Rodney added as he finished downloading the data and input the commands to shut down the facility.

"In the meantime, let's take her home."

A/N: Yes I know, I've started another story but I just couldn't help myself! As usual it's focused on Elizabeth as she's my favourite. Please let me know what you think, it's deeply appreciated.


	2. Shattered Reality

Chapter 2: Shattered Reality 

The city was a buzz of liveliness when John and the team returned through the Gate. Keller had been waiting with a stretcher and a med team and John lowered Elizabeth onto it gently. He followed them all the way to the infirmary as Keller insisted that he get checked out to ensure that Elizabeth hadn't been made infectious. It felt a bit like déjà vu, taking the long walk through the corridors. Just the reverse journey he and Elizabeth had taken when they left for that fateful mission a year ago.

He was nervous. Too many thoughts were flying about his head. Plus the security team that also escorted them seemed to be on edge. Not that he blamed them. If it really was their Elizabeth, then even with all the Replicators destroyed, she could still pose a threat to them all. She was part Replicator, and who knew what they had done to her.

Still he was trying to be positive. If it really was their Elizabeth then he had finally fulfilled his promise to bring her home. He had so much apologising to do. So much to tell her about what had happened during her absence. He knew her journey would be difficult, fitting into normal and putting things back to the way they were but he wouldn't abandon her ever again. He would finally put things right for her.

But he knew he was getting ahead of himself. Though this walk seemed to be taking an eternity. It was just the apprehension. The wait. It always was with these situations. After four years in the Pegasus Galaxy he should have been used to it. But he doubted he ever would. When they finally arrived in the infirmary, Keller ushered Elizabeth into an isolation room to begin scans and to verify her identity. He was separated from her and placed in his own isolation room and placed under a scanner.

It didn't take long to discern that everything was ok and he wasn't under attack. John practically bolted from the room back into the main infirmary. Heading to where Elizabeth was being seen to. As soon as he got there Keller exited the room and guided him away towards the video feeds. Too much like she had when she'd told him Elizabeth might not survive.

"It's her." She simply states, anticipating his question. He felt like jumping with glee but he could tell by her tone that all was not well. "As far I can tell, there's been no physical trauma. But she's still unconscious and I have no idea why."

"What did they do to her?" He asks but it's more to himself than anyone else. He's looking at the screens, at Elizabeth's serene calm face as she slumbers. His brow furrows with worry. He couldn't help but feel this was the calm before the storm.

"I wish I knew." Keller answers anyway a sigh escaping her lips. She felt responsible for what happened to Elizabeth. After all it was her idea to reactivate the nanites in the first place.

Silence enveloped them as they both stared at the monitors. Time seems to stop as they think about the ramifications of Elizabeth being back on Atlantis. Though obviously relived that she back where she belongs, they both know there's a lot to figure out.

Unfortunately for them they're about to realise just how bumpy and long this road is going to be.

John and Keller see on the screen that Elizabeth's eyes snap open and her green eyes dart around, taking in all her surroundings. A nurse notices her awakening and goes over to talk to her, to reassure her that she is safe when trouble stirs.

Just as the nurse reaches her Elizabeth grabs hold lf her arm and twists her around. Locking her arm behind the nurse' back, threatening to snap the bone. She vaults off the bed and slams the poor lady into the wall.

Keller is too stunned to move but John is already moving and so are the other medical and security personnel. The other nurses go to aid of their colleague while the two security officers go to restrain Elizabeth. As John enters the room he his shocked to see Elizabeth smashing her elbow into one of the men's faces and trying to escape the other one's grasp.

"Elizabeth!" He calls her name to try and get her attention and is about to dive into the fray when she wrenches herself free and throws the marine over her shoulder onto the floor.

She screams at him and the next thing he knows, she's tackling him to the ground with her hands around his neck. His hands automatically grab her wrists trying to pry her off him but she's stronger than she appears.

"Just stop it! Just end this!" She screams at him as her nails dig into his skin about to draw blood.

He doesn't understand what she means and he's desperately trying to get air into his lungs, to yell at her to stop.

"Elizabeth calm down!" Teyla's voice comes from somewhere and then Ronan's arms wrap around her and tear her from him.

Keller runs in with a syringe, obviously containing a sedative and Ronan roughly holds out Elizabeth's left arm and the kind doctor instantly injects it. He leans forward and watches in astonishment as she looks at all of them with deep hatred engrained into her once lovely green eyes.

"Curse you." Elizabeth spits out and her body slowly gives up struggling to escape. Her eyes lock onto his and her voice waivers and begins to slur. "I'll get you one of these days…Oberoth."

A/N: Sorry that it's been so long since I updated this story and the fact this Chapter is fairly short but I've been busy on other projects but I'm hoping to work on this more now. Let me know what you think. Thanks.


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